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- PDB-2iz5: FUNCTION AND STRUCTURE OF THE MOLYBDENUM COFACTOR CARRIER PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 2iz5
TitleFUNCTION AND STRUCTURE OF THE MOLYBDENUM COFACTOR CARRIER PROTEIN MCP FROM CHLAMYDOMONAS REINHARDTII
ComponentsMOCO CARRIER PROTEIN
KeywordsMETAL TRANSPORT
Function / homologySLOG cluster4 / SLOG cluster4 family / : / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Molybdenum cofactor carrier protein
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsFischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Function and Structure of the Molybdenum Cofactor Carrier Protein from Chlamydomonas Reinhardtii.
Authors: Fischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Ataya, F.S. / Galvan, A. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOCO CARRIER PROTEIN
B: MOCO CARRIER PROTEIN
C: MOCO CARRIER PROTEIN
D: MOCO CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)71,5554
Polymers71,5554
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-62.5 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.313, 75.881, 126.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MOCO CARRIER PROTEIN


Mass: 17888.670 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DL41 / References: UniProt: Q8RV61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97962
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 53717 / % possible obs: 94.5 % / Observed criterion σ(I): 2.1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.29→65.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.408 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE PARTIALLY TRACED WITH ALA RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1471 5.1 %RANDOM
Rwork0.215 ---
obs0.218 27469 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--2.77 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.29→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 0 163 4618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224504
X-RAY DIFFRACTIONr_bond_other_d0.0010.024432
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9876108
X-RAY DIFFRACTIONr_angle_other_deg0.954310291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7735630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29126.29124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6331511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined0.2410.21092
X-RAY DIFFRACTIONr_nbd_other0.1920.24475
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22085
X-RAY DIFFRACTIONr_nbtor_other0.090.22918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1221.53966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34124953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00931487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0914.51155
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 84
Rwork0.248 1602
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.291-0.72541.36093.9572-0.82965.0731-0.1671-0.03290.36810.4158-0.2202-0.0043-0.20530.00620.3873-0.06470.03520.1169-0.1571-0.0494-0.204819.44174.76222.3764
24.22981.23460.17414.65480.42583.4261-0.13980.0402-0.4606-0.0207-0.0115-0.05860.37460.29460.1513-0.0395-0.0096-0.0454-0.0552-0.0035-0.164123.7268-8.5335-14.6709
32.69130.516-1.17311.2224-0.49363.0072-0.0299-0.26070.1375-0.02320.00820.3701-0.0233-0.06020.0217-0.1173-0.005-0.0639-0.0685-0.0348-0.054117.8522-1.1552-7.6211
43.41430.81470.4315.6506-0.73593.3224-0.0803-0.03890.6351-0.1085-0.17760.1294-0.3576-0.20510.2579-0.0766-0.02440.0542-0.0892-0.0229-0.132445.74088.3076-14.109
52.95610.77571.16442.2640.09463.60340.0548-0.1657-0.007-0.045-0.0523-0.2990.08290.0179-0.0026-0.11890.01580.0203-0.03940.0022-0.089650.30041.6472-6.425
65.2802-1.042-1.35083.7785-0.1643.279-0.3244-0.2108-0.4710.51220.04760.23730.11840.0720.27680.01010.1101-0.0378-0.07590.0511-0.149347.0958-4.457423.4002
75.0106-0.6708-1.8112.970.34593.2788-0.00550.06960.27670.08250.1546-0.1931-0.0096-0.0131-0.1491-0.1270.0361-0.0968-0.06930.02-0.199749.61453.716915.6829
83.7388-0.462.56662.15720.81183.68650.01660.2089-0.02860.097-0.04060.25440.1798-0.040.024-0.116-0.03090.1324-0.0702-0.0481-0.130517.9783-3.310814.5072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D5 - 69
2X-RAY DIFFRACTION2A4 - 73
3X-RAY DIFFRACTION3A76 - 166
4X-RAY DIFFRACTION4B1 - 71
5X-RAY DIFFRACTION5B74 - 166
6X-RAY DIFFRACTION6C4 - 69
7X-RAY DIFFRACTION7C75 - 166
8X-RAY DIFFRACTION8D73 - 166

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